A cascaded approach to normalising gene mentions in biomedical literature.

ABSTRACT: Linking gene and protein names mentioned in the literature to unique identifiers in referent genomic databases is an essential step in accessing and integrating knowledge in the biomedical domain. However, it remains a challenging task due to lexical and terminological variation, and ambiguity of gene name mentions in documents. We present a generic and effective rule-based approach to link gene mentions in the literature to referent genomic databases, where pre-processing of both gene synonyms in the databases and gene mentions in text are first applied. The mapping method employs a cascaded approach, which combines exact, exact-like and token-based approximate matching by using flexible representations of a gene synonym dictionary and gene mentions generated during the pre-processing pha

SUBMITTER: Yang H 

PROVIDER: S-EPMC2241928 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature